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jmzquantml -- A Java API for mzQuantML


7, July 2014 -- jmzquantml 1.0.0-1.0.5 has been released. Full Java documentation can be found in http://jmzquantml.googlecode.com/svn/trunk/src/docs/api/1.0.0-1.0.5/index.html.


General

jmzquantml is a JAVA API for reading and writing mzQuantML file which is designed for reording quantitative proteomic data and meta-data.

Download JAR file

As Googlecode has terminated the download service on January 2014, new release after version 1.0.0-1.0.3 cannot be found in download section from left column. The latest jar file can be downloaded from http://code.google.com/p/jmzquantml/source/browse/#svn%2Fmaven%2Frepo%2Fuk%2Fac%2Fliv%2Fjmzquantml. Before download, refer to "release notes" for latest news.


Documentations

Here are the API documentation links to all API versions. http://jmzquantml.googlecode.com/svn/trunk/src/docs/api/index.htm

How to use jmzquantml artifact in maven

jmzquantml artifact is currently using Googlecode host as its maven repository. To use it, add the following to your POM:

First, add jmzquantml dependency (check the latest version):

  <dependency>
     <groupId>uk.ac.liv</groupId>
     <artifactId>jmzquantml</artifactId>
     <version>1.0.0-1.0.5</version>
  </dependency>
Second, add wagon-svn extension (current version 1.12) in <build> tag:
  <extensions>
     <extension>
        <groupId>org.jvnet.wagon-svn</groupId>
        <artifactId>wagon-svn</artifactId>
        <version>1.12</version>
     </extension>
  </extensions>
Finally, add plugin repository and jmzquantml repository:
  <pluginRepositories>
     <pluginRepository>
        <id>maven2-repository.dev.java.net</id>
        <name>Java.net Repository for Maven</name>
        <url>http://download.java.net/maven/2/</url>
     </pluginRepository>
  </pluginRepositories>
  <repositories>
     <repository>
        <id>jmzquantml-maven-repo</id>
        <name>Maven Repository for jmzquantml release</name>
        <url>http://jmzquantml.googlecode.com/svn/maven/repo</url>
     </repository>
  </repositories>

Examples

To help users to familiarise with the API, we have generated some example classes to illustrate the most important features. They can be found from here.


Citation

The paper of jmzquantml API has been published in Proteomics. If you would like to cite jmzquantml in your paper, please use the following citation:

Plain

Qi, D., Krishna, R. and Jones, A. R. (2014), The jmzQuantML programming interface and validator for the mzQuantML data standard. Proteomics, 14: 685–688. doi: 10.1002/pmic.201300281

Bibtex

@article {QI14:PROTEOMICS,
author = {Qi, Da and Krishna, Ritesh and Jones, Andrew R},
title = {The jmzQuantML programming interface and validator for the mzQuantML data standard},
journal = {PROTEOMICS},
volume = {14},
number = {6},
issn = {1615-9861},
url = {http://dx.doi.org/10.1002/pmic.201300281},
doi = {10.1002/pmic.201300281},
pages = {685--688},
keywords = {Bioinformatics, Java API, mzQuantML, Proteomics Standards Initiative, XML},
year = {2014},
}

Contact

Dr Da Qi (D.Qi at liverpool.ac.uk , replace at with @)

Dr Andy Jones (Andrew.Jones at liverpool.ac.uk, replace at with @)

last update: 22/08/2014

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